Contacts of the helix formed by residues 41 - 56 (chain A) in PDB entry 2RD9
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A HIS 3.7 10.3 - - - -
32A GLN* 3.6 31.3 + - + +
33A CYS 3.4 8.7 - - - -
34A ASN* 4.1 9.4 - - + +
39A THR 5.2 0.4 - - - +
40A TRP* 1.3 75.5 - - - +
42A VAL* 1.3 65.2 + - - +
43A TYR* 3.5 6.6 + - - +
44A GLU* 3.0 40.6 + - - +
45A VAL* 3.0 21.9 + - - +
153A SER* 5.6 0.2 - - - -
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.8 34.1 - - + -
30A TRP 3.5 17.0 - - - +
31A HIS* 3.2 19.9 + - + +
33A CYS* 3.1 19.5 + - - +
41A THR* 1.3 73.3 - - - +
43A TYR* 1.3 65.0 + - - +
45A VAL* 3.1 14.1 + - - +
46A VAL* 3.1 14.1 + - + +
90A ILE* 5.2 0.9 - - + -
150A ILE* 3.9 43.0 - - + +
153A SER* 4.2 4.2 - - - -
154A MSE 4.0 2.9 - - + -
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Residues in contact with TYR 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ASP* 5.8 0.4 - - - -
31A HIS* 3.0 16.8 + - + +
32A GLN* 4.5 17.0 - - - +
41A THR* 3.6 7.6 - - - +
42A VAL* 1.3 76.2 - - - +
44A GLU* 1.3 66.0 + - + +
46A VAL* 3.1 7.3 + - - +
47A VAL* 2.9 44.2 + - + +
85A SER 3.3 8.3 + - - -
86A ASN* 3.5 35.0 + - + -
88A VAL 2.6 29.5 + - - -
90A ILE* 4.1 41.3 - - + -
93A ARG* 3.0 27.3 + - + +
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Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A THR 4.6 1.2 - - - +
40A TRP* 3.4 17.4 - - + +
41A THR* 3.0 44.3 + - - +
43A TYR* 1.3 80.9 - - + +
45A VAL* 1.3 61.1 + - - +
47A VAL* 3.5 5.8 + - + -
48A HIS* 2.9 17.8 + - - +
86A ASN* 6.0 4.6 - - + -
304A GOL 2.7 56.1 + - - +
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Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A TRP* 4.0 12.6 - - + +
41A THR 3.0 15.3 + - - +
42A VAL* 3.1 8.0 + - - +
44A GLU* 1.3 73.0 - - - +
46A VAL* 1.3 60.9 + - - +
48A HIS* 3.2 7.6 + - - +
49A LEU* 3.0 30.0 + - + +
146A HIS* 3.7 37.2 - - + +
149A GLN* 3.6 32.8 - - + +
150A ILE* 3.8 26.0 - - + +
153A SER* 5.9 0.4 - - - +
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Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 4.4 9.9 - - + -
23A LEU* 4.1 17.9 - - + -
42A VAL 3.1 13.8 + - - +
43A TYR* 3.1 9.5 + - - +
45A VAL* 1.3 72.0 - - - +
47A VAL* 1.3 66.5 + - - +
49A LEU* 3.2 9.2 + - - +
50A ILE* 3.1 26.6 + - + +
90A ILE* 4.7 7.0 - - + -
93A ARG* 3.9 26.5 - - + -
94A PHE* 4.2 21.3 - - + -
97A PHE* 5.4 6.3 - - + -
150A ILE* 4.0 17.3 - - + -
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A TYR* 2.9 45.1 + - + +
44A GLU* 3.7 9.0 - - + +
45A VAL 3.4 0.2 - - - -
46A VAL* 1.3 74.4 - - - +
48A HIS* 1.3 62.5 + - - +
50A ILE* 3.2 13.3 + - + +
51A GLU* 3.1 21.6 + - + +
84A GLN* 3.7 35.9 - - + +
93A ARG* 3.7 23.3 - - + +
304A GOL 3.9 11.4 - - - +
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Residues in contact with HIS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A TRP* 3.4 27.8 - + + -
44A GLU 2.9 17.9 + - - +
45A VAL 3.5 4.0 - - - +
47A VAL* 1.3 73.1 - - - +
49A LEU* 1.3 60.8 + - - +
51A GLU* 3.1 13.7 + - - +
52A ALA* 2.9 25.5 + - - +
142A HIS* 3.2 5.5 + + - -
146A HIS* 3.2 29.8 - + - -
300A NI 2.2 36.0 - - + +
304A GOL 3.8 7.9 + - - +
174B ASP* 4.8 0.2 - - - -
-10D HIS* 3.4 25.6 + + - -
-9D HIS* 3.2 15.7 - + - -
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A THR* 5.0 4.3 - - + -
19A LEU* 3.6 30.3 - - + -
45A VAL* 3.0 22.7 + - + +
46A VAL* 3.2 8.0 + - - +
48A HIS* 1.3 75.6 - - - +
50A ILE* 1.3 62.6 + - - +
52A ALA* 3.4 6.8 + - + +
53A GLU* 3.2 26.3 + - - +
97A PHE* 4.0 23.0 - - + -
101A ARG* 5.5 0.7 - - - +
142A HIS* 3.8 28.3 - - + +
143A ASP* 4.0 20.4 - - - +
146A HIS* 4.0 28.7 - - + -
147A ILE* 5.5 0.4 - - + +
150A ILE* 5.2 0.7 - - + -
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Residues in contact with ILE 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A VAL* 3.1 16.1 + - + +
47A VAL* 3.3 10.8 - - - +
48A HIS 3.2 0.2 - - - -
49A LEU* 1.3 76.1 - - - +
51A GLU* 1.3 63.2 + - - +
53A GLU* 3.0 19.9 + - - +
54A LYS* 3.3 21.0 + - - +
84A GLN* 5.7 4.0 - - - +
93A ARG* 3.2 49.6 - - + +
96A GLU* 3.6 23.6 - - - +
97A PHE* 3.7 27.6 - - + +
100A LEU* 3.7 17.9 - - + -
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Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 3.1 14.4 + - + +
48A HIS* 3.1 17.5 + - - +
50A ILE* 1.3 77.7 - - - +
52A ALA* 1.3 55.7 + - - +
54A LYS* 3.0 12.5 + - + +
55A THR* 2.9 40.6 + - + +
81A HIS* 3.8 21.6 - - + +
84A GLN* 5.5 4.8 - - - +
-12D HIS* 2.5 37.6 + - - -
-10D HIS* 2.9 34.5 + - - +
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A HIS 2.9 10.3 + - - +
49A LEU* 3.6 10.3 - - + +
51A GLU* 1.3 75.9 - - - +
53A GLU* 1.3 60.1 + - - +
56A ASN* 3.1 26.0 + - + +
57A TRP* 3.5 32.1 + - + +
142A HIS* 4.0 14.1 - - + +
-10D HIS* 3.5 27.0 - - + +
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Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU 3.2 15.0 + - - +
50A ILE 3.0 11.5 + - - +
52A ALA* 1.3 79.2 - - - +
54A LYS* 1.3 57.7 - - - +
56A ASN 5.0 0.2 - - - -
57A TRP* 4.0 5.3 + - - -
58A ILE* 5.3 0.9 + - - +
59A PRO* 5.0 6.4 - - - +
97A PHE* 3.7 17.7 - - + -
100A LEU* 3.9 21.1 - - + +
101A ARG* 2.8 51.4 + - - +
104A ASN* 2.8 47.6 + - - +
139A TRP* 3.3 14.9 + - - -
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Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ILE* 3.6 20.2 - - + +
51A GLU* 3.0 12.4 + - + +
53A GLU* 1.3 79.9 - - - +
55A THR* 1.3 59.5 + - - +
56A ASN 3.9 0.4 - - - -
59A PRO* 3.6 15.8 - - - +
84A GLN* 5.3 9.3 + - - +
96A GLU* 3.1 29.2 + - - -
100A LEU* 3.7 27.1 - - + -
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Residues in contact with THR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLU* 2.9 24.2 + - + +
54A LYS* 1.3 78.7 - - - +
56A ASN* 1.3 63.1 + - - +
59A PRO* 3.8 15.9 - - - +
60A ARG* 5.4 0.5 - - - +
76A PHE* 3.6 17.6 - - + -
79A PHE* 5.2 4.2 - - - -
81A HIS* 3.7 25.8 + - - -
-10D HIS* 3.5 41.3 - - + +
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Residues in contact with ASN 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ALA* 3.1 17.1 + - + +
54A LYS 3.9 0.4 - - - -
55A THR* 1.3 77.6 - - - +
57A TRP* 1.3 96.7 + - + +
58A ILE 3.6 1.3 - - - -
59A PRO* 3.4 3.2 - - - +
60A ARG* 3.1 37.1 + - - +
76A PHE* 3.5 21.3 - - + -
-10D HIS* 3.1 32.5 + - - +
-9D HIS* 3.4 22.2 + - - -
-6D GLU* 5.1 0.4 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il